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Detailed information for vg0505864665:

Variant ID: vg0505864665 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 5864665
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGTGTGGTGTGGCGTGGTGGTGGAGTCATGGGTGTATGACTCCACTCGTCAGGGTTAAGATCCTGATACCTACAAATATTACAATATATGTATGCGGG[C/T]
TTTCTATAGGATTTCAGTGAGATCAGAGATGTGCCACATCCATATAGGTCTTTTATCGGTATATGATGAGGGTAACATATTCTATGCACACATCCATCTT

Reverse complement sequence

AAGATGGATGTGTGCATAGAATATGTTACCCTCATCATATACCGATAAAAGACCTATATGGATGTGGCACATCTCTGATCTCACTGAAATCCTATAGAAA[G/A]
CCCGCATACATATATTGTAATATTTGTAGGTATCAGGATCTTAACCCTGACGAGTGGAGTCATACACCCATGACTCCACCACCACGCCACACCACACCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.70%	4.00%	0.25%	0.00%	NA
All Indica	2759	92.90%	6.70%	0.40%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.30%	4.20%	0.50%	0.00%	NA
Indica II	465	93.50%	6.00%	0.43%	0.00%	NA
Indica III	913	90.80%	9.00%	0.22%	0.00%	NA
Indica Intermediate	786	93.00%	6.50%	0.51%	0.00%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0505864665	C -> T	LOC_Os05g10680-LOC_Os05g10690	intergenic_region ; MODIFIER	silent_mutation	Average:86.561; most accessible tissue: Zhenshan97 root, score: 95.335	N	N	N	N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0505864665	C	T	-0.01	-0.03	-0.03	0.01	0.01	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0505864665	3.50E-06	3.50E-06	mr1190	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	1.39E-06	NA	mr1245	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	2.20E-06	2.26E-07	mr1245	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	1.93E-07	2.70E-07	mr1373	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	6.60E-08	6.60E-08	mr1373	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	NA	6.37E-06	mr1616	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	NA	9.42E-06	mr1648	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	9.35E-08	1.53E-09	mr1697	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0505864665	2.19E-07	7.02E-09	mr1697	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251